Conserved non-coding element analysis in M.opercularis

Repository containing scripts used for analysing conserved non-coding elements in the M.opercularis genome.

Aim

The aim of the project is to find conserved non-coding elements (CNE) in the M.opercularis genome which can be associated with the evolution of the labyrinth organ. This is done by whole genome alignments of multiple teleost species with and without the labyrinth organ, calling the CNEs and testing acceleration of the CNE sequences in the lineage with labyrinth organ. Some subsequent analyses for mostly visualization are performed with custom R scripts.

Repo structure

scripts/ - contains the scripts used during the analysis.

misc/ - contains ancilliary files for the analysis.

Order of scripts

1. OrthoFinder2 was used to generate the species tree:

orthofinder -t 20 -a 20 -f /projects/ferenc.kagan/CNE_PFARs/00_raw_data/orthofinder

2. scripts/MAF_Processing_and_Phylo_Analysis.sh
3. scripts/CNE_Annotation_and_Enrichment_Analysis.R